Abstract
Key message
Coexpression network revealing genes with Co-variation Expression pattern (CE) and those with Top rank of Expression fold change (TE) played different roles in responding to new environment of Miscanthus lutarioriparius.
Abstract
Variation in gene expression level, the product of genetic and/or environmental perturbation, determines the robustness-to-plasticity spectrum of a phenotype in plants. Understanding how expression variation of plant population response to a new field is crucial to domesticate energy crops. Weighted Gene Coexpression Network Analysis (WGCNA) was used to explore the patterns of expression variation based on 72 Miscanthus lutarioriparius transcriptomes from two contrasting environments, one near the native habitat and the other in one harsh domesticating region. The 932 genes with Co-variation Expression pattern (CE) and other 932 genes with Top rank of Expression fold change (TE) were identified and the former were strongly associated with the water use efficiency (r ≥ 0.55, P ≤ 10−7). Functional enrichment of CE genes were related to three organelles, which well matched the annotation of twelve motifs identified from their conserved noncoding sequence; while TE genes were mostly related to biotic and/or abiotic stress. The expression robustness of CE genes with high genetic diversity kept relatively stable between environments while the harsh environment reduced the expression robustness of TE genes with low genetic diversity. The expression plasticity of CE genes was increased less than that of TE genes. These results suggested that expression variation of CE genes and TE genes could account for the robustness and plasticity of acclimation ability of Miscanthus, respectively. The patterns of expression variation revealed by transcriptomic network would shed new light on breeding and domestication of energy crops.
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Abbreviations
- WGCNA:
-
Weighted gene coexpression network analysis
- CE:
-
Co-variation expression pattern
- TE:
-
Top rank of expression fold change
- JH:
-
Jiangxia in Hubei Province
- QG:
-
Qingyang in Gansu Province
- WUE:
-
Water use efficiency
- A:
-
CO2 assimilation rate
- E:
-
Transpiration rate
- FPKM:
-
Expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced
- ANOVA:
-
Analysis of variance
- TO:
-
Topological overlap
- ME:
-
Module eigengene
- GO:
-
Gene ontology
- KEGG:
-
Kyoto encyclopedia of genes and genomes
- SNPs:
-
Single-nucleotide polymorphism
- dS :
-
The synonymous substitution rates
- dN :
-
Non-synonymous substitution rates
- E p :
-
Average expression level
- E d :
-
Expression diversity
- π:
-
Genetic diversity
- NC:
-
Non-differential change
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Acknowledgements
This study was supported by the National Key Research and Development Program of China (No. 2016YFC0500905), the grants from the National Natural Science Foundation of China (31000147; 31400284), the Project for Autonomous Deployment of the Wuhan Botanical Garden (55Y755271G02) and the Science and Technology Service Network Initiative of the Chinese Academy of Sciences (KFJ-EW-STS-061).
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TS conceived and designed the experiments. SX, ZS, JY, CL and LK performed the experiments. SX, ZS and WL performed data analysis. SX, CT, JY and TS wrote the manuscript. All authors read and approved the final manuscript.
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**ng, S., Tao, C., Song, Z. et al. Coexpression network revealing the plasticity and robustness of population transcriptome during the initial stage of domesticating energy crop Miscanthus lutarioriparius. Plant Mol Biol 97, 489–506 (2018). https://doi.org/10.1007/s11103-018-0754-5
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DOI: https://doi.org/10.1007/s11103-018-0754-5